Bahrad A. Sokhansanj

Dec 9, 2024 | biorxiv.org | Mohammadsaleh Refahi |Bahrad A. Sokhansanj |Joshua Chang Mell |James Brown

AbstractAnalysis of genomic and metagenomic sequences is inherently more challenging than that of amino acid sequences due to the higher divergence among evolutionarily related nucleotide sequences, variable k-mer and codon usage within and among genomes of diverse species, and poorly understood selective constraints. We introduce Scorpio, a versatile framework designed for nucleotide sequences that employs contrastive learning to improve embeddings.

Jul 23, 2024 | biorxiv.org | Mohammadsaleh Refahi |Bahrad A. Sokhansanj |Joshua Chang Mell |James Brown

AbstractAnalyzing genomic and genetic sequences on the DNA level can be challenging due to the limited alphabet and sequence similarity varies depending on the labeling task, which makes tasks dependent on different evolutionary rates. In addition, metagenomic data poses significant challenges due to the vast diversity of taxa and genes within a microbiome.